PDB-5uy3: Crystal structure of human Fab PGT144, a broadly reactive and pot...

ID or keywords:

Entry

Database: PDB / ID: 5uy3

Title

Crystal structure of human Fab PGT144, a broadly reactive and potent HIV-1 neutralizing antibody

Components

Antibody PGT144 Fab heavy chain
Antibody PGT144 Fab light chain

Keywords

IMMUNE SYSTEM / Antibody / HIV Env glycoprotein

Function / homology

Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta

Function and homology information

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.9 Å

Authors

Julien, J.-P. / Lee, J.H. / Wilson, I.A.

Funding support

United States, 5items

Organization	Grant number	Country
California HIV/AIDS Research Program Dissertation Award	D12-SRI-353	United States
Scripps CHAVI-ID	UM1 AI100663	United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	AI110657	United States
International AIDS Vaccine Initiative		United States
Bill & Melinda Gates Foundation	OPP1115782 and OPP1084519	United States

Citation

Journal: Immunity / Year: 2017
Title: A Broadly Neutralizing Antibody Targets the Dynamic HIV Envelope Trimer Apex via a Long, Rigidified, and Anionic β-Hairpin Structure.
Authors: Jeong Hyun Lee / Raiees Andrabi / Ching-Yao Su / Anila Yasmeen / Jean-Philippe Julien / Leopold Kong / Nicholas C Wu / Ryan McBride / Devin Sok / Matthias Pauthner / Christopher A Cottrell / ...
Abstract: Broadly neutralizing antibodies (bnAbs) to HIV delineate vaccine targets and are prophylactic and therapeutic agents. Some of the most potent bnAbs target a quaternary epitope at the apex of the ...

History

Deposition	Feb 23, 2017	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Apr 19, 2017	Provider: repository / Type: Initial release
Revision 1.1	May 3, 2017	Group: Database references
Revision 1.2	Sep 6, 2017	Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3	Dec 11, 2019	Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4	Oct 4, 2023	Group: Data collection / Database references / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.5	Nov 15, 2023	Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.6	Nov 20, 2024	Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	5uy3.cif.gz	343.4 KB	Display	PDBx/mmCIF format
PDB format	pdb5uy3.ent.gz	280.8 KB	Display	PDB format
PDBx/mmJSON format	5uy3.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	5uy3_validation.pdf.gz	459.4 KB	Display	wwPDB validaton report
Full document	5uy3_full_validation.pdf.gz	476.4 KB	Display
Data in XML	5uy3_validation.xml.gz	32.6 KB	Display
Data in CIF	5uy3_validation.cif.gz	43.5 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/uy/5uy3 ftp://data.pdbj.org/pub/pdb/validation_reports/uy/5uy3	HTTPS FTP

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Related structure data

Related structure data	8643C 8644C 5v8lC 5v8mC 3u1sS 4rqq S: Starting model for refinement C: citing same article (ref.)
Similar structure data	4rqq-1 3u1s-d 4rqq-3 6e9q-1 4rqq-2 5uxq-1 6e9k-d 6e9q-2 6rlo-2 4n9g-4 Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#21 - Sep 2001 Antibodies similarity (1) #256 - Apr 2021 SARS-CoV-2 Spike and Antibodies similarity (1)

Deposited unit

L: Antibody PGT144 Fab light chain

H: Antibody PGT144 Fab heavy chain

B: Antibody PGT144 Fab light chain

A: Antibody PGT144 Fab heavy chain

98.9 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

L: Antibody PGT144 Fab light chain

H: Antibody PGT144 Fab heavy chain

defined by author&software
Evidence: gel filtration
49.4 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: Antibody PGT144 Fab light chain

A: Antibody PGT144 Fab heavy chain

defined by author&software
49.4 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	57.600, 67.550, 69.550
Angle α, β, γ (deg.)	82.04, 74.89, 81.26
Int Tables number	1
Space group name H-M	P1

#1: Antibody	Antibody PGT144 Fab light chain Mass: 23560.322 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#2: Antibody	Antibody PGT144 Fab heavy chain Mass: 25874.729 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
Has protein modification	Y

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 2.63 Å³/Da / Density % sol: 53.31 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: JCSG F8

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.033 Å
Detector	Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Dec 12, 2011
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.033 Å / Relative weight: 1
Reflection	Resolution: 2.9→40 Å / Num. obs: 21292 / % possible obs: 96.6 % / Redundancy: 2.1 % / R_merge(I) obs: 0.16 / Net I/σ(I): 5.5
Reflection shell	Resolution: 2.9→3 Å / Redundancy: 2.1 % / R_merge(I) obs: 0.39 / Mean I/σ(I) obs: 1.9 / % possible all: 96.9

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Processing

Software

Name	Version	Classification
PHENIX	(1.10_2155: ???)	refinement
XDS		data reduction
XDS		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 3U1S

3u1s

Resolution: 2.9→36.293 Å / SU ML: 0.52 / Cross valid method: FREE R-VALUE / σ(F): 2.08 / Phase error: 30.9

	R_factor	Num. reflection	% reflection
R_free	0.2821	1064	5 %
R_work	0.2409	-	-
obs	0.243	21284	96.59 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å

Refinement step

Cycle: LAST / Resolution: 2.9→36.293 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6856	0	0	0	6856

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.003	7021
X-RAY DIFFRACTION	f_angle_d	0.619	9541
X-RAY DIFFRACTION	f_dihedral_angle_d	16.244	4171
X-RAY DIFFRACTION	f_chiral_restr	0.043	1062
X-RAY DIFFRACTION	f_plane_restr	0.004	1215

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
2.9-3.032	0.4131	133	0.3203	2541	X-RAY DIFFRACTION	97
3.032-3.1917	0.3289	133	0.2934	2530	X-RAY DIFFRACTION	97
3.1917-3.3915	0.3088	135	0.2648	2566	X-RAY DIFFRACTION	97
3.3915-3.6532	0.3066	132	0.2565	2508	X-RAY DIFFRACTION	97
3.6532-4.0204	0.2821	132	0.242	2508	X-RAY DIFFRACTION	96
4.0204-4.6012	0.2648	133	0.2143	2529	X-RAY DIFFRACTION	96
4.6012-5.7932	0.2071	134	0.2	2524	X-RAY DIFFRACTION	97
5.7932-36.2959	0.2681	132	0.2223	2514	X-RAY DIFFRACTION	96

Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

ID	L11 (°²)	L12 (°²)	L13 (°²)	L22 (°²)	L23 (°²)	L33 (°²)	S11 (Å °)	S12 (Å °)	S13 (Å °)	S21 (Å °)	S22 (Å °)	S23 (Å °)	S31 (Å °)	S32 (Å °)	S33 (Å °)	T11 (Å²)	T12 (Å²)	T13 (Å²)	T22 (Å²)	T23 (Å²)	T33 (Å²)	Origin x (Å)	Origin y (Å)	Origin z (Å)
1	0.0218	0.0116	0.0039	0.022	-0.0105	0.0014	0.011	0.0398	-0.1344	-0.0425	0.0548	0.0041	-0.0007	0.0749	0	0.3759	0.0353	-0.0416	0.5146	-0.063	0.2508	10.3934	-6.7183	26.9997
2	0.0099	-0.022	0.0283	0.0009	-0.0311	0.0188	0.1708	-0.1909	-0.1348	-0.1547	0.0373	0.1924	-0.0932	0.1315	0	0.2353	0.0251	-0.0167	0.3304	-0.2396	0.0619	10.2752	1.4274	26.3122
3	0.0059	-0.0144	0.0044	-0.0165	-0.0262	0.0492	0.1063	0.1062	-0.0346	-0.0324	0.0076	-0.051	-0.0645	-0.1134	0	0.2427	-0.0062	-0.001	0.2079	-0.0069	0.2619	-2.2987	7.9728	58.5671
4	0.0344	0.0133	-0	0.0315	0.0064	-0.0165	0.0489	0.0116	0.0091	0.0863	-0.0775	0.0503	-0.0294	0.0778	-0	0.1805	-0.013	0.005	0.1255	0.0029	0.2043	-2.8689	8.1292	61.1826
5	-0.002	-0.0052	0.0071	-0.0043	-0.0137	0.0111	-0.0782	-0.0151	0.0776	-0.0508	0.0837	0.0428	-0.1154	-0.0787	-0	0.5268	0.0872	0.0916	0.5688	-0.1116	0.4016	-9.8679	14.5082	20.3876
6	-0.0789	0.0166	-0.0035	-0.001	-0.005	0.0152	-0.1703	0.2111	0.1588	-0.2471	-0.3802	-0.2142	0.1752	0.1692	0	-0.7094	0.2275	-0.3363	-0.8353	-0.8949	-0.8441	-6.0857	2.411	14.861
7	0.0001	-0.0217	0.0388	-0.0143	0.025	-0.0044	0.0025	0.0991	-0.2339	0.0746	-0.3028	-0.025	-0.2617	-0.046	-0	0.1577	0.1132	0.0119	-0.3921	-0.0358	0.1369	-6.6486	21.6551	51.1424
8	0.0191	-0.0238	0.025	0.0228	0.0178	0.0346	0.0872	0.1017	-0.1257	0.0166	0.1496	0.0293	0.0588	0.0023	0	0.3065	-0.0867	0.064	0.3546	-0.0202	0.2021	7.2054	33.605	23.5332
9	0.0331	0.016	0.0181	0.0121	-0.0117	-0.0033	0.2088	0.1206	-0.2141	-0.0595	-0.032	-0.2328	-0.1295	-0.1425	0	-0.4384	-0.3223	0.0694	0.3036	0.1089	0.257	7.8734	33.5888	17.8268
10	0.0002	-0.0047	-0.0009	0.0289	0.0121	0.0277	0.1174	0.0343	0.1586	0.1914	-0.0411	0.1503	0.0715	0.1488	0	0.1417	-0.0274	-0.0143	0.1384	0.0452	0.1879	25.0661	39.3036	-10.5953
11	0.045	0.0329	0.0199	0.0452	-0.0204	0.0022	0.0276	-0.0551	-0.0357	-0.0855	-0.0082	-0.0149	0.0372	-0.0407	0	0.3371	0.0185	0.0455	0.1787	0.0452	0.2354	23.5382	36.112	-12.0249
12	0.0028	0.0079	0.0003	0.0027	0.0001	0.0021	-0.0054	0.023	-0.0383	-0.0097	0.0176	-0.0035	0.0061	0.0677	0	0.2288	-0.0873	0.2235	0.4877	-0.0313	0.3752	37.3722	38.3915	22.2988
13	0.004	0.0051	0.0048	0.0031	-0.0018	0.0029	-0.0218	0.0589	0.0381	-0.0355	-0.0134	-0.0742	-0.0237	0.0226	0	0.4006	-0.0047	0.0769	0.234	-0.0087	0.1885	27.3805	46.0765	37.5154
14	0.0058	0.0153	-0.0031	-0.0102	0.0062	-0.0011	0.0036	0.057	0.0134	-0.0363	0.0486	0.0409	0.0893	0.0125	-0	0.1516	0.1037	-0.0409	0.344	0.0531	0.1818	24.4901	33.1705	25.6176
15	-0.001	0.0021	-0.0047	0.0039	-0.0088	0.0035	0.0744	0.0336	-0.1473	-0.0028	0.033	0.0102	0.0051	0.0392	0	0.4664	-0.0793	-0.0161	0.095	0.1565	0.1198	26.7853	29.2903	35.6052
16	-0.0199	0.0532	0.0177	-0.0024	-0.0039	0.0192	0.0861	0.1578	-0.1299	0.144	0.1816	0.0374	0.2097	-0.1076	0	0.0892	0.1417	-0.1534	0.0638	0.1479	-0.0063	28.1557	32.88	32.9478
17	0.0118	0.0056	0.0122	0.0073	0.0058	0.0091	-0.0033	0.1282	0.1289	0.0393	-0.2015	0.1022	0.0515	-0.0087	0	0.3915	-0.0687	-0.0269	0.2968	0.0525	0.1871	19.6014	30.8395	40.5476
18	-0.0149	-0.0583	0.0458	-0.0396	-0.0042	0.0144	0.0392	-0.066	0.0165	0.0627	0.0113	0.0661	-0.0836	0.0539	0	0.1083	-0.0192	0.0203	0.1403	0.0113	0.1754	30.5305	49.1955	-1.7449

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'L' and (resid 2 through 32 )
2	X-RAY DIFFRACTION	2	chain 'L' and (resid 33 through 102 )
3	X-RAY DIFFRACTION	3	chain 'L' and (resid 103 through 160 )
4	X-RAY DIFFRACTION	4	chain 'L' and (resid 161 through 212 )
5	X-RAY DIFFRACTION	5	chain 'H' and (resid 4 through 32 )
6	X-RAY DIFFRACTION	6	chain 'H' and (resid 33 through 116 )
7	X-RAY DIFFRACTION	7	chain 'H' and (resid 117 through 218 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 2 through 61 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 62 through 113 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 114 through 150 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 151 through 212 )
12	X-RAY DIFFRACTION	12	chain 'A' and (resid 4 through 20 )
13	X-RAY DIFFRACTION	13	chain 'A' and (resid 21 through 32 )
14	X-RAY DIFFRACTION	14	chain 'A' and (resid 33 through 51 )
15	X-RAY DIFFRACTION	15	chain 'A' and (resid 52 through 61 )
16	X-RAY DIFFRACTION	16	chain 'A' and (resid 62 through 100E)
17	X-RAY DIFFRACTION	17	chain 'A' and (resid 100G through 116 )
18	X-RAY DIFFRACTION	18	chain 'A' and (resid 117 through 218 )

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